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Ted Laderas, PhD
Assistant Professor, Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology
Researcher, OHSU Knight Cancer Institute
I am an Assistant Professor in the Division of Bioinformatics and Computational Biology in the Department of Medical Informatics and Clinical Epidemiology at OHSU (BCB/DMICE) and a member of the OHSU Knight Cancer Institute. My research focus is on the Systems Biology of Complex Diseases. I use integrative modeling approaches across OMICs types to achieve this.I am also passionate about teaching students to think about data, and have taught Data Science to a variety of groups, including graduate students, post-docs, staff, and clinicians. I am also an RStudio Certified Trainer in both the tidyverse and shiny.
Education
PhD, Biomediical Informatics
Oregon Health & Science University
Portland, OR
2014 - 2009
- Dissertation: Connecting Genotypes to Drug Sensitivities in HER2 Positive Cancer Cell Lines
M.S., Biomedical Informatics
Oregon Health & Science University
Portland, OR
2004 - 2002
- Thesis: Developing and validating a tool for microarray cluster analysis
B.A., Chemistry
Reed College
Portland, OR
1998 - 1994
- Thesis: Resonance-Raman Spectroscopy, Chromium Hexacarbonyl, and Me: A Tale of Intrigue
Software
surrogateMutation
N/A
N/A
Current - 2014
- R Package for mapping mutations and copy number alterations to networks and associated statistics. http://dx.doi.org/10.5281/zenodo.17303
flowDashboard
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N/A
Current - 2017
- Visualization framework in R/Shiny and processing pipeline for CyTOF and high dimensionality flow cytometry data.
Courses
Teaching and education are a passion of mine. I teach in a number of courses at OHSU. I spend a lot of time developing coursework/workshops in a variety of Data Science Topics. Most of my material is freely available to be reused by other instructors.
BMI569: Data Analytics
Biomedical Informatics, Oregon Health & Science University
Portland, OR
Current - 2015
- Course co-director. Hybrid course co-taught with Kaiser Permanente Insight group.
- Winner of the Sakai Torchbearer Award 2020. Multiple nominations from students.
- Audience is both clinicians and bioinformaticans.
BMI535/635: Management and Processing of Large Scale Data
Biomedical Informatics, Oregon Health & Science University
Portland, OR
Current - 2020
- Course co-director. A course that focuses on UNIX scripting, parallel computing, and large scale databases.
BMI507: Ready for R
Biomedical Informatics, Oregon Health & Science University
Portland, OR
Current - 2020
- Course Director. A gentle introduction to visualization, data transformation, and statistics using R and the tidyverse.
- Course is open to anyone at https://ready4r.netlify.app/mailing
- Currently over 1000 external students have enrolled.
NEUS643: Stats for Neuroscientists
Neuroscience Graduate Program, Oregon Health & Science University
Portland, OR
Current - 2020
- Course Director. An introduction to image processing, statistics, and machine learning focusing on confocal microscopy data.
- Lecture/Active Learning Labs using RStudio.cloud.
BMI551/651 Bioinformatics and Computational Biology II: Statistical Methods
Biomedical Informatics, Oregon Health & Science University
Portland, OR
2019 - 2015
- Course co-instructor. Provided drop-in sessions for R/Bioconductor programming and general tutoring.
HMSP410/PHE427: Introduction to Health Informatics
Portland State University
Portland, OR
2018 - 2017
- Course co-director. A gentle introduction to relevant data science and informatics concepts for Public Health Education students.
- Includes sections on data literacy, genomics, and metadata
NEUS: Python Bootcamp for Neuroscientists
Neuroscience Graduate Program, Oregon Health & Science University
N/A
2018 - 2018
- Week long introduction to Python for non-computational neuroscientists.
Educational Resources
RBootcamp
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Current - 2015
- Online Interactive Introduction to the Tidyverse
- Written with Jessica Minnier
A gRadual Introduction to Shiny
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Current - 2017
- Workshop introducing basic interactive visualization and dashboard building using the Shiny framework for R
- Written with Jessica Minnier
- Used by multiple colleges, including Reed College and Lehmann College
Clinical Data Wrangling
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Current - 2017
- Multi-day workshop on understanding clinical data quality issues through both didactic lecturing and active data exploration.
- Written with Eilis Boudreau and Nicole Weiskopf.
- Given as an intro to both our incoming clinical and bioinformatics students.
Selected Publications, Posters, and Talks
My research interests are complex diseases, precision medicine, applications of systems science (including network analysis and modeling), and applying data integration to difficult and high-impact translational research questions. These questions include immune system profiling in both infectious disease (tuberculosis) and Acute Myeloid Leukemia, understanding drug sensitivity in the context of multiple cancer types (AML, Colorectal, Breast and Head and Neck Cancer), and quantifying expression differences in alcoholic preference. I have worked with a large number of datatypes (high-throughput immunophenotyping, proteomics, expression, genomic, and functional drug screen data) and have focused on methods and frameworks integrating these datatypes within the biological and clinical context of these translational research questions. My training in biomedical informatics as a master’s student in Biomedical Informatics, as an NLM Predoctoral Fellow, and as a NLM Postdoctoral fellow has enabled me to communicate with a wide variety of collaborators by giving me a strong background in Cancer Biology, Software Development, and Clinical Systems. Additionally, I am a strong advocate for Open Science initiatives, most notably the effort for reproducibility in scientific analysis. To this end, I have developed multiple novel software pipelines that transparently process data from raw data to through the final stages of analysis.
Illuminating Biological Pathways for Drug Targeting in Head and Neck Squamous Cell Carcinoma
PLOS One
N/A
2020
- Gabrielle Choonoo, Aurora S. Blucher, Samuel Higgins, Mitzi Boardman, Sophia Jeng, Christina Zheng, James Jacobs, Ashley Anderson, Steven Chamberlin,Nathaniel Evans, Myles Vigoda,Benjamin Cordier, Jeffrey W. Tyner, Molly Kulesz-Martin, Shannon K. McWeeney, and Ted Laderas.
- Senior Author. Did code review of entire workflow and published the workflow as an RMarkdown Notebook at mybinder.org
CSF1R inhibitors exhibit anti-tumor activity in acute myeloid leukemia by blocking paracrine signals from support cells
Blood
N/A
2019
- David K Edwards, Kevin Watanabe-Smith, Angela Rofelty, Alisa Damnernsawad, Ted Laderas, Adam Lamble, Evan F Lind, Andy Kaempf, Motomi Mori, Mara Rosenberg, Amanda d”Almeida, Nicola Long, Anupriya Agarwal, David Tyler Sweeney, Marc Loriaux, Shannon K McWeeney, Jeffrey W Tyner.
Immunogenomic Exploration of the Acute Myeloid Leukemia Microenvironment Identifies Determinants of T-Cell Fitness.
Blood
N/A
2018
- Lauren K Brady, David Soong, Evan F Lind, Yoko Kosaka, Adam J Lamble, Michael Schaffer, Brendan P Hodkinson, Clare Lefave, Ted Laderas, Shannon K McWeeney, Homer Adams, Yann Abraham, Pegah Safabakhsh, Jeffrey W Tyner, Brian J Druker, Fei Huang.
Training future biocurators through data science trainings and open educational resources.
F1000 Research
N/A
2017
- Nicole Vasilevsky, Ted Laderas, Jackie Wirz, Bjorn Pederson, David A Dorr, William Hersh, Shannon McWeeney, Melissa Haendel.
Teaching data science fundamentals through realistic synthetic clinical cardiovascular data
Biorkv
N/A
2017
- Ted Laderas, Nicole Vasilevsky, Bjorn Pederson, Shannon McWeeney, Melissa Haendel, and David Dorr.
- Contribution: First author: helped conceive study, designed bayesian network, developed course material based on dataset.
The Consensus Molecular Subtypes of Colorectal Cancer.
Nature Medicine
N/A
2015
- Justin Guinney, Rodrigo Dienstmann, Xin Wang, Aurélien de Reyniès, Andreas Schlicker, Charlotte Soneson, Laetitia Marisa, Paul Roepman, Gift Nyamundanda, Paolo Angelino, Brian M. Bot, Jeffrey S. Morris, Iris Simon, Sarah Gerster, Evelyn Fessler, Felipe de Sousa e Melo, Edoardo Missiaglia, Hena Ramay, David Barras, Krisztian Homicsko, Dipen Maru, Ganiraju C. Manyam, Bradley Broom, Valerie Boige, Ted Laderas, Ramon Salazar, Joe W. Gray, Douglas Hanahan, Josep Tabernero, Rene Bernards, Stephen H. Friend, Pierre Laurent-Puig, Jan P. Medema, Anguraj Sadanandam, Lodewyk Wessels, Mauro Delorenzi, Scott Kopetz, Louis Vermeulen, and Sabine Tejpar.
- Contribution: mapped and analyzed OMICs data to consensus cancer subtypes.
Between Pathways and Networks lies Context.
Science Progress
N/A
2015
- Ted Laderas, Guanming Wu, and Shannon McWeeney.
Consensus framework for exploring microarray data using multiple clustering methods.
OMICS
N/A
2007
- Ted Laderas and Shannon McWeeney
Selected Data Science Writing
I regularly blog about education, data science, and mental health in a variety of places.
Rebuilding the RBootcamp and Generating R Tutorials
RStudio Education Blog
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2020
- Story about building our interactive RBootcamp using Ines Montani’s interactive R/Python Framework.
- Authored with Florencia D’Andrea and Jessica Minnier
RStudioConf 2019: Education and Organizations
Personal Blog
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2019
- Story about presenting our poster about interactive data science education and educational resources/talks at RStudioConf 2019
Notes on the RStudio Instructor Training Experience
Personal Blog
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2019
- Story about becoming an RStudio Certified Instructor in the Tidyverse and Shiny
What we learned teaching Python to Neuroscience Students
Personal Blog
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2018
- Notes on organizing an intro Python course for Neuroscience Students
So You’ve Accidentally Checked a Large File Into Git
Personal Blog
N/A
2018
- Notes on fixing your Git history using the BFG
Some Lessons we Learned Running Cascadia R
Personal Blog
N/A
2017
- Notes on organizing and running the first NW regional R Conference, Cascadia R
Selected Press (About)
Selected Press (By)
Positions and Work Experience
Assistant Professor
Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science Univeristy
Portland, OR
Current - 2015
NLM Postdoctoral Fellow, Division of Bioinformatics and Computational Biology
Oregon Health & Science Univeristy
Portland, OR
2015 - 2014
Visiting Scientist
Sage Bionetworks
Seattle, WA
2015 - 2014
NLM Predoctoral Fellow
Medical Informatics and Clinical Epidemiology, Oregon Health & Science Univeristy
N/A
2014 - 2009
Bioinformatics Developer/Project Manager, OHSU Knight Cancer Institute
Oregon Health & Science University
Portland, OR
2009 - 2003
Teaching Assistant/Computer Programmer/Server Admin, Medical Informatics and Clinical Epidemiology
Oregon Health & Science University
Portland, OR
2002 - 2001
Research Assistant/Computer Programmer, Department of Molecular Medicine
Oregon Health & Science University
Portland, OR
2001 - 1999
- Developed and extended real time image processing pipeline using LabView. Conducted surface tension experiments using lung surfactant components
Research Assistant/Teaching Assistant
Gerrity Lab
Reed College
1998 - 1996
- TA in Instrumentation Lab
- Conducted research using resonance raman spectroscopy/
- Programmed in LabView/Igor